Daniel E. Deatherage

TL;DR: How to run the open-source breseq computational pipeline to identify and annotate genetic differences found in whole-genome and whole-population NGS data from haploid microbes where a high-quality reference genome is available is described.

TL;DR: Nonsynonymous mutations, intergenic mutations, insertions and deletions are overrepresented in the long-term populations, further supporting the inference that most mutations that reached high frequency were favoured by selection.

TL;DR: An algorithm for identifying structural variation from DNA resequencing data is implemented as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes and is able to reliably predict structural variation with modest read-depth coverage of the reference genome.

TL;DR: Large-scale rearrangements clearly influenced genomic evolution in twelve Escherichia coli populations propagated in a glucose-limited environment for over 25 years, providing these populations with genetic plasticity reminiscent of that observed in some pathogenic bacteria.

TL;DR: The sequenced complete genomes from 30 Escherichia coli lineages that evolved for 2,000 generations in one of five environments that differed only in the temperatures they experienced demonstrate that genomic signatures of adaptation can be highly specific, even with respect to subtle environmental differences, but that this imprint may become obscured over longer timescales.